report.enabled = true
conda.enabled = true
conda.useMicromamba = true

workDir = 'nxwork'

profiles {
  dropseq {
    params.cb_whitelist = null
    params.cb_len = 12
    params.umi_len = 8
  }
  
  tenx3pv3 {
    params.cb_whitelist = '/home/gjsx/append-ssd/work/cb_whitelist/3M-february-2018.txt'
    params.cb_len = 16
    params.umi_len = 12
  }
  
  tenx3pv2 {
    params.cb_whitelist = '/home/gjsx/append-ssd/work/cb_whitelist/737K-august-2016.txt'
    params.cb_len = 16
    params.umi_len = 10
  }
  
  tenx5p {
    params.cb_whitelist = '/home/gjsx/append-ssd/work/cb_whitelist/737K-august-2016.txt'
    params.cb_len = 16
    params.umi_len = 10
    params.add_5p_conf = '--soloBarcodeMate 1 --clip5pNbases 39 0'
    params.add_cr_conf = "--outFilterScoreMin 30 --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIfiltering MultiGeneUMI_CR --soloUMIdedup 1MM_CR"
  }
  
  sgp3cb {
    params.cb_whitelist = '/home/gjsx/append-ssd/work/cb_whitelist/corrected_p3_barcodes.txt'
    params.cb_len = 17
    params.umi_len = 12
  }
  
  human {
    params.star_index = '/home/gjsx/append-ssd/work/star_hs_v46'
  }
  
  mouse {
    params.star_index = '/home/gjsx/append-ssd/work/star_m35'
  }
} 
